mesh animation & boolean: avoid bugs & glitches (Cycles)?
The sides disappearing is because the cube you are using for the road domain is a little bit too small, scale it about 0.03 bigger on the Y axis and you will get a better boolean result.

Your second problem is the caps on the ends of your road mesh. By using an array modifier you get these repeated along the road, this leads to the ends appearing and disapearing as it moves along. For this remove the faces at both ends and apply the array modifier, then recap the ends.